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Yorodumi- PDB-1oqg: Crystal structure of the D63E mutant of the N-lobe human transferrin -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oqg | ||||||
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Title | Crystal structure of the D63E mutant of the N-lobe human transferrin | ||||||
Components | Serotransferrin | ||||||
Keywords | TRANSPORT PROTEIN / transferrin mutagenesis / iron binding / anion binding | ||||||
Function / homology | Function and homology information iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade / basal plasma membrane / osteoclast differentiation / ferric iron binding / actin filament organization / ferrous iron binding / Post-translational protein phosphorylation / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / regulation of protein stability / regulation of iron ion transport / HFE-transferrin receptor complex / cellular response to iron ion / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / Clathrin-mediated endocytosis / antibacterial humoral response / iron ion transport / cytoplasmic vesicle / secretory granule lumen / blood microparticle / intracellular iron ion homeostasis / vesicle / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Baker, H.M. / He, Q.-Y. / Brigg, S.K. / Mason, A.B. / Baker, E.N. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Structural and functional consequences of binding site mutations in transferrin: crystal structures of the Asp63Glu and Arg124Ala mutants of the N-lobe of human transferrin Authors: Baker, H.M. / He, Q.-Y. / Briggs, S.K. / Mason, A.B. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oqg.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oqg.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/1oqg ftp://data.pdbj.org/pub/pdb/validation_reports/oq/1oqg | HTTPS FTP |
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-Related structure data
Related structure data | 1oqhC 1a8eS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37229.293 Da / Num. of mol.: 1 / Fragment: N-lobe / Mutation: D63E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNUT / Cell (production host): Baby hamster kidney (BHK) CELLS / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: P02787 |
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#2: Chemical | ChemComp-CO3 / |
#3: Chemical | ChemComp-FE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.31 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 3350, potassium acetate, ammonium bicarbonate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Details: used microseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: May 8, 2002 / Details: osmic confocal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 27976 / Num. obs: 26077 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 10.2 / Num. unique all: 2511 / % possible all: 90.8 |
Reflection | *PLUS Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 91.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A8E Resolution: 1.9→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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